Comments (2)
That could be something complex but I wonder if something went wrong when making the database. Could you try deleting accessionTaxa.sql
and reinstalling with prepareDatabase('accessionTaxa.sql')
(note that'll download some big files and take a while to process)?
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Thank you for the tip. There is some problem with how my machine was regenerating the sql database. (My solution was to just use the sql database generated on my co-workers machine).
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Related Issues (20)
- read.names.sql for common names HOT 2
- Assignment of taxonomy to blast hits HOT 1
- error: no such column: tmp.query.accession HOT 1
- Manual preparation of database HOT 1
- Error in preparing accessionTaxa.sql with prepareDatabase() HOT 10
- Get all bacterial species HOT 2
- Questions for the issue of taxonomizr package being terminated during operation HOT 1
- Error: disk I/O error In addition: Warning message: Couldn't set synchronous mode: disk I/O error HOT 5
- accessionToTaxa returns a single NA when the input contains too many accession ID HOT 3
- Error in downloading database using prepareDatabase HOT 9
- prepareDatabase('accessionTaxa.sql') downloading names and nodes with getnamesandnodes() error: HOT 9
- Error:database is locked with prepareDatabase HOT 3
- Cannot get taxonomizr to work HOT 4
- Pointing R to an already prepared database HOT 4
- Unable to query SQL database when built with `getAccessions=FALSE` HOT 2
- Does this tool do LCA? HOT 1
- Exclude species with no rank HOT 1
- error in prepareDatabase HOT 3
- Error in prepareDatabase('accessionTaxa.sql'), change in url? HOT 3
- Download failed with error: "FTP response timeout". HOT 1
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